Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell RNA and TCR profiling of tetramer sorted mouse mLN and IELs.

ABSTRACT: Single cell RNA and TCR profiling of tetramer sorted mouse mLN and IELs.

PROVIDER: PRJNA804878 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR17957700_1.fastq.gz	Fastqsanger.gz
	SRR17957700_2.fastq.gz	Fastqsanger.gz
	SRR17957701_1.fastq.gz	Fastqsanger.gz
	SRR17957701_2.fastq.gz	Fastqsanger.gz
	SRR17957702_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 80

Similar Datasets

Single cell RNA and TCR profiling of tetramer sorted mouse mLN and IELs.

Project description:We utilized H2-I-Ab tetramers to isolate CD4 T cells from mice to characterize the functional characteristics of ileal intraepithelial T cells and their lymphoid counterparts in the corresponding draining lymph nodes (mLN). Non-CD4 T cells (B220+, CD11b+, CD11c+, F4/80+, CD8a+) were excluded before FACS-sorting of CD45+CD3+CD4+ tetramer-specific T cells discriminated by double-positive staining with dual-labeled tetramer fluorophores. We recovered tetramer+ and tetramer- IELs and mLN T cells, and profiled them by single-cell RNA and TCR sequencing.

2022-09-01 | GSE196426 | GEO

Mtb HLA-E tetramer sorted CD8+ T-cells have a diverse TCR repertoire

Project description:Mtb HLA-E tetramer sorted CD8+ T-cells have a diverse TCR repertoire

| PRJNA989142 | ENA

Mtb HLA-E tetramer sorted CD8+ T-cells have a diverse TCR repertoire

Project description:HLA-E molecules can present self and pathogen-derived peptides to both NK-cells and T-cells. T-cells that recognize HLA-E peptides via their T-cell receptor (TCR) are termed donor-unrestricted T-cells due to restricted allelic variation of HLA-E. The composition and repertoire of HLA-E TCRs is not known so far. We performed TCR sequencing on CD8+ T-cells from 21 individuals recognizing HLA-E tetramers (TM) folded with 2 Mtb HLA-E restricted peptides. We sorted HLA-E Mtb TM+ and TMCD8+ T-cells directly ex vivo and performed bulk RNA-sequencing and single cell TCR sequencing. The identified TCR repertoire was diverse and showed no conservation between and within individuals. TCRs selected from our single cell TCR sequencing data could be activated upon HLA-E/peptide stimulation, although not robust, reflecting potentially weak interactions between HLA-E peptide complexes and TCRs. Thus, HLA-E Mtb specific T-cells have a highly diverse TCR repertoire.

2024-02-04 | GSE236154 | GEO

Total and cholera toxin B-tetramer specific T cells from Peyer's patches and mesenteric lymph nodes

Project description:T cells were separately isolated from MLN and PP from two naive mice, and T cells binding to a cholera toxin B subunit specific MHC II tetramer from mice orally immunized with cholera toxin 7 days or boosted 5 days with a second dose of cholera toxin. Cells were purified using flow cytometric cell sorting and 3´ (n=5) or 5´ (n=5) libraries were constructed using the 10X workflow. From 5´libraries TCR libraries were also constructed and sequenced.

2022-06-22 | E-MTAB-11805 | biostudies-arrayexpress

MLN

Project description:MLN

| PRJEB7634 | ENA

RNA libraries of sorted CD8+ memory T cells from the spleen and RNA libraries of sorted IELs from the small intestine of C57BL/6J mice

Project description:Intraepithelilal lymphocytes (IELs) are located at the intestinal barrier where they can offer swift protection against invading pathogens. However, they are kept in a heightened state of activation resembling effector T cells, but without cytokine production or clonal proliferation. They also posses altered metabolic pathways than CD8+ memory T cells from spleen. With differentially expressed gene analysis of intestinal IELs and CD8+ memory T cells from spleen, we confirmed increased expression of metabolic enzymes involved in lipid uptake and lipid metabolism in IELs compared with CD8+ memory T cells. This was particularly the case for enzymes involved in mevalonate, lanosterol and cholesterol synthesis pathways, suggesting increased lipid metabolite generation. Differential gene expression showed also strong predisposition for cytotoxic potential that IELs possess in comparison to CD8+ memory T cell.

2018-07-10 | E-MTAB-6510 | biostudies-arrayexpress

Single cell RNA-seq of human CD8+ T cells binding the IAV HLA-A24/PB1 498-505 tetramer

Project description:PBMCs from 4 donors were stained with the influenza A virus HLA-A24/PB1 498-505 tetramer. Two donors (non-LIFT8 and non-LIFT12) showed TCR independent KIR binding to tetramers whereas the other two donors (Non-LIFT14 and Non-LIFT10) showed TCR specific binding. Cells were single-cell sorted on a BD Aria III into 96-well plates containing 0.5 μl dNTP mix (10 mM), 0.5 μl oligo-dT pri- mer (5 μM), and 1 μl lysis buffer (prepared by adding 1 μl RNase inhibitor to 19 μl Triton X-100 solution, 0.2% v/v).

2021-04-08 | E-MTAB-10109 | biostudies-arrayexpress

Transcription profiling of mouse small intestine intraepithelial lymphocytes (IEL) vs. TCR ab+ CD8b+ and TCR gd+ cells

Project description:Mouse small intestine intraepithelial lymphocytes (IEL) that express a ab TCR and CD8aa homodimers are an enigmatic T cell subset, as their specificity and in vivo function remain to be defined. To gain insight into the nature of these cells, we performed global gene expression profiling using microarray analysis, combined with PCR and flow cytometry to determine the level of expression of selected genes. Using these methods, TCR ab+ CD8aa IEL were compared to their TCR ab+ CD8b+ and TCR gd+ counterparts. Experiment Overall Design: In this study, the three IEL populations were isolated by cell sorting from a pool of IELs from 20 mice. RNA from each IEL subset was used to probe one microarray. A replicate experiment was performed on a seperate occasion using a new pool of 20 mice and three additional microarrays were used.

2008-06-13 | E-GEOD-5355 | biostudies-arrayexpress

Murine gamma delta intraepithelial lymphocyte response to type I IFN and TCR blockade

Project description:Interferon alpha (IFNa) is a pro-inflammatory cytokine that is rapidly upregulated as part of an innate immune response. Gamma delta intraepithelial lymphocytes (gd IEL) mount a rapid antimicrobial response to luminal microorganisms and previous report indicate that the T cell receptor (TCR) of these cells is constantly triggered at steady-state. We assessed the contribution of tonic TCR activation in response to acute, systemic IFNa administration among murine gd IELs. Our data demonstrate that inhibiting basal TCR signaling has a minimal effect on the transcriptional profile of gd IELs and acute IFNa exposure induces antiviral gene programs independent of TCR signaling.

2024-10-01 | GSE262121 | GEO

Single cell gene expression analysis of mouse colon ΤCRδ+CD8α+ and TCRβ+CD8α+ intraepitehlial lymphocytes (IELs)

Project description:TCF-1 is highly expressed in colon T- IELs.Tο understand the role of TCF-1 in regulating the gene expression of colon CD8+ T IELs, we isolated and sorted CD8α+TCRδ+ and CD8α+TCRβ+ from colons of E8Ιcre-Transgentic Tcf7 floxed mice or control Tcf7 floxed mice.

2023-10-06 | GSE202691 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data